Install fails with Cython 3.0.2

[dwfmarchant]

Looks like the install crashes with Cython 3 that was released last month. Downgrading to the previous Cython release (v0.29.35) fixes things.

(simpeg) ➜  ~ pip list
Package           Version
----------------- -------
Cython            3.0.2
geoana            0.5.0
libdlf            0.2.0
numpy             1.25.2
packaging         23.1
pip               23.2.1
scipy             1.11.2
setuptools        68.0.0
setuptools-scm    7.1.0
tomli             2.0.1
typing_extensions 4.7.1
wheel             0.40.0
(simpeg) ➜  ~ pip install discretize
Collecting discretize
  Using cached discretize-0.9.0.tar.gz (1.1 MB)
  Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy>=1.20 in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from discretize) (1.25.2)
Requirement already satisfied: cython>=0.29 in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from discretize) (3.0.2)
Requirement already satisfied: setuptools_scm in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from discretize) (7.1.0)
Requirement already satisfied: scipy>=1.8 in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from discretize) (1.11.2)
Requirement already satisfied: packaging>=20.0 in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from setuptools_scm->discretize) (23.1)
Requirement already satisfied: setuptools in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from setuptools_scm->discretize) (68.0.0)
Requirement already satisfied: typing-extensions in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from setuptools_scm->discretize) (4.7.1)
Requirement already satisfied: tomli>=1.0.0 in ./.virtualenvs/simpeg/lib/python3.10/site-packages (from setuptools_scm->discretize) (2.0.1)
Building wheels for collected packages: discretize
  Building wheel for discretize (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [67 lines of output]
      Compiling discretize/_extensions/interputils_cython.pyx because it changed.
      Compiling discretize/_extensions/tree_ext.pyx because it changed.
      Compiling discretize/_extensions/simplex_helpers.pyx because it changed.
      [1/3] Cythonizing discretize/_extensions/interputils_cython.pyx
      /Users/dmarchant/.virtualenvs/simpeg/lib/python3.10/site-packages/Cython/Compiler/Main.py:384: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /private/var/folders/vv/bfm07t4x54s2y2bf10ls0tr40000gn/T/pip-install-dsjxa4xy/discretize_3fb1281a136c459cafe6b1e44807860c/discretize/_extensions/interputils_cython.pxd
        tree = Parsing.p_module(s, pxd, full_module_name)
      [2/3] Cythonizing discretize/_extensions/simplex_helpers.pyx
      [3/3] Cythonizing discretize/_extensions/tree_ext.pyx
      warning: discretize/_extensions/tree_ext.pyx:5357:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5357:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:17: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:38: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:45: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:52: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:59: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5358:66: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5488:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5488:25: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5488:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5488:37: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:17: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:24: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:31: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:38: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:45: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:52: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:59: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5489:66: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5490:17: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5490:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5490:29: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5490:35: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:19: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:33: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:40: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:47: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:54: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:61: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.
      warning: discretize/_extensions/tree_ext.pyx:5752:68: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line.

      Error compiling Cython file:
      ------------------------------------------------------------
      ...
                  diagonal_balance = self._diagonal_balance
              cdef bool diag_balance = diagonal_balance

              #Wrapping function so it can be called in c++
              cdef void * func_ptr = <void *> function
              self.wrapper.set(func_ptr, _evaluate_func)
                                         ^
      ------------------------------------------------------------

      discretize/_extensions/tree_ext.pyx:505:35: Cannot assign type 'int (void *, Cell *) except? -1 nogil' to 'int (*)(void *, Cell *) noexcept'. Exception values are incompatible. Suggest adding 'noexcept' to type 'int (void *, Cell *) except? -1 nogil'.
      warning: discretize/_extensions/tree_ext.pyx:754:19: Index should be typed for more efficient access
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/private/var/folders/vv/bfm07t4x54s2y2bf10ls0tr40000gn/T/pip-install-dsjxa4xy/discretize_3fb1281a136c459cafe6b1e44807860c/setup.py", line 127, in <module>
          metadata["ext_modules"] = cythonize(extensions)
        File "/Users/dmarchant/.virtualenvs/simpeg/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
          cythonize_one(*args)
        File "/Users/dmarchant/.virtualenvs/simpeg/lib/python3.10/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
          raise CompileError(None, pyx_file)
      Cython.Compiler.Errors.CompileError: discretize/_extensions/tree_ext.pyx
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for discretize
  Running setup.py clean for discretize
Failed to build discretize
ERROR: Could not build wheels for discretize, which is required to install pyproject.toml-based projects

[omid-b]

I think it is the time to move to a more modern metadata and setup configuration format to avoid these issues and make discretize more OS-independent and future-proof. I opened #336 that will address this one too...

[jcapriot]

I believe this is fixed on main, as we use cython 3.0 to build it.